Package | Description |
---|---|
eu.etaxonomy.cdm.api.facade | |
eu.etaxonomy.cdm.api.service | |
eu.etaxonomy.cdm.api.service.dto | |
eu.etaxonomy.cdm.api.utility | |
eu.etaxonomy.cdm.io.specimen | |
eu.etaxonomy.cdm.io.specimen.abcd206.in | |
eu.etaxonomy.cdm.io.specimen.gbif.in | |
eu.etaxonomy.cdm.io.taxonx | |
eu.etaxonomy.cdm.io.taxonx2013 | |
eu.etaxonomy.cdm.model.molecular |
Provides classes for DNA samples and related sequences.
|
eu.etaxonomy.cdm.model.name |
Provides classes for nomenclature and typification.
|
eu.etaxonomy.cdm.model.occurrence |
Provides classes for specimens, collections and field units.
|
eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence | |
eu.etaxonomy.cdm.persistence.dao.occurrence |
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
DerivedUnitFacade.addDuplicate(Collection collection,
java.lang.String catalogNumber,
java.lang.String accessionNumber,
TaxonName storedUnder,
PreservationMethod preservation)
Creates a duplicate specimen which derives from the same derivation event
as the facade specimen and adds collection data to it (all data available
in DerivedUnit and Specimen.
|
DerivedUnit |
DerivedUnitFacade.innerDerivedUnit()
Returns the derived unit itself.
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<DerivedUnit> |
DerivedUnitFacade.getDuplicates() |
Modifier and Type | Method and Description |
---|---|
void |
DerivedUnitFacade.addDuplicate(DerivedUnit duplicateSpecimen) |
java.lang.String |
DerivedUnitFacadeCacheStrategy.getTitleCache(DerivedUnit derivedUnit) |
java.lang.String |
DerivedUnitFacadeCacheStrategy.getTitleCache(DerivedUnit derivedUnit,
boolean skipFieldUnit) |
static DerivedUnitFacade |
DerivedUnitFacade.NewInstance(DerivedUnit derivedUnit)
Creates a derived unit facade for a given derived unit using the default
configuration.
|
static DerivedUnitFacade |
DerivedUnitFacade.NewInstance(DerivedUnit derivedUnit,
DerivedUnitFacadeConfigurator config) |
void |
DerivedUnitFacade.removeDuplicate(DerivedUnit duplicateSpecimen) |
Modifier and Type | Method and Description |
---|---|
java.util.List<DerivedUnit> |
IOccurrenceService.getAllChildDerivatives(SpecimenOrObservationBase<?> specimen)
Returns all child derivatives of the given specimen.
|
java.util.List<DerivedUnit> |
OccurrenceServiceImpl.getAllChildDerivatives(SpecimenOrObservationBase<?> specimen) |
java.util.List<DerivedUnit> |
IOccurrenceService.getAllChildDerivatives(java.util.UUID specimenUuid)
Returns all child derivatives of the given specimen.
|
java.util.List<DerivedUnit> |
OccurrenceServiceImpl.getAllChildDerivatives(java.util.UUID specimenUuid) |
java.util.List<UuidAndTitleCache<DerivedUnit>> |
IOccurrenceService.getDerivedUnitUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern)
Retrieves the
UUID and the string representation (title cache) of all
DerivedUnit s found in the data base. |
java.util.List<UuidAndTitleCache<DerivedUnit>> |
OccurrenceServiceImpl.getDerivedUnitUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
java.util.Map<DerivedUnit,java.util.Collection<SpecimenTypeDesignation>> |
IOccurrenceService.listTypeDesignations(java.util.Collection<DerivedUnit> specimens,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
SpecimenTypeDesignation s which have the given specimens as a type specimen. |
java.util.Map<DerivedUnit,java.util.Collection<SpecimenTypeDesignation>> |
OccurrenceServiceImpl.listTypeDesignations(java.util.Collection<DerivedUnit> specimens,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
PreservedSpecimenDTO |
IOccurrenceService.assemblePreservedSpecimenDTO(DerivedUnit derivedUnit)
Assembles a
PreservedSpecimenDTO for the given derived unit. |
PreservedSpecimenDTO |
OccurrenceServiceImpl.assemblePreservedSpecimenDTO(DerivedUnit derivedUnit) |
PreservedSpecimenDTO |
OccurrenceServiceImpl.assemblePreservedSpecimenDTO(DerivedUnit derivedUnit,
FieldUnitDTO fieldUnitDTO) |
DerivedUnitFacade |
IOccurrenceService.getDerivedUnitFacade(DerivedUnit derivedUnit,
java.util.List<java.lang.String> propertyPaths) |
DerivedUnitFacade |
OccurrenceServiceImpl.getDerivedUnitFacade(DerivedUnit derivedUnit,
java.util.List<java.lang.String> derivedUnitFacadeInitStrategy) |
java.lang.String |
IOccurrenceService.getMostSignificantIdentifier(DerivedUnit derivedUnit)
Returns the most significant identifier for the given
DerivedUnit . |
java.lang.String |
OccurrenceServiceImpl.getMostSignificantIdentifier(DerivedUnit derivedUnit) |
java.util.Collection<SpecimenTypeDesignation> |
IOccurrenceService.listTypeDesignations(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
SpecimenTypeDesignation s which have the given specimen as a type specimen. |
java.util.Collection<SpecimenTypeDesignation> |
OccurrenceServiceImpl.listTypeDesignations(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listTypeDesignationTaxa(DerivedUnit specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listTypeDesignationTaxa(DerivedUnit specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listTypeDesignationTaxa(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa with a
SpecimenTypeDesignation with the given specimen as a type specimen. |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listTypeDesignationTaxa(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa with a
SpecimenTypeDesignation with the given specimen as a type specimen. |
boolean |
IOccurrenceService.moveDerivate(SpecimenOrObservationBase<?> from,
SpecimenOrObservationBase<?> to,
DerivedUnit derivate) |
boolean |
OccurrenceServiceImpl.moveDerivate(SpecimenOrObservationBase<?> from,
SpecimenOrObservationBase<?> to,
DerivedUnit derivate) |
Modifier and Type | Method and Description |
---|---|
java.util.Map<DerivedUnit,java.util.Collection<SpecimenTypeDesignation>> |
IOccurrenceService.listTypeDesignations(java.util.Collection<DerivedUnit> specimens,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
SpecimenTypeDesignation s which have the given specimens as a type specimen. |
java.util.Map<DerivedUnit,java.util.Collection<SpecimenTypeDesignation>> |
OccurrenceServiceImpl.listTypeDesignations(java.util.Collection<DerivedUnit> specimens,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Constructor and Description |
---|
DNASampleDTO(DerivedUnit derivedUnit) |
PreservedSpecimenDTO(DerivedUnit derivedUnit) |
Modifier and Type | Class and Description |
---|---|
class |
DerivedUnitConverter<TARGET extends DerivedUnit> |
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
DerivedUnitConverter.oldDerivedUnit()
Returns the derived unit which was the source entity for the conversion.
|
Constructor and Description |
---|
DerivedUnitConverter(DerivedUnit source) |
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
SpecimenImportStateBase.getDerivedUnitBase() |
Modifier and Type | Method and Description |
---|---|
void |
SpecimenImportStateBase.setDerivedUnitBase(DerivedUnit derivedUnitBase) |
Modifier and Type | Method and Description |
---|---|
void |
SpecimenImportReport.addAlreadyExistingSpecimen(java.lang.String unitId,
DerivedUnit derivedUnit) |
void |
SpecimenImportReport.addDerivate(DerivedUnit parent,
DerivedUnit child,
SpecimenImportConfiguratorBase config) |
void |
SpecimenImportReport.addDerivate(DerivedUnit parent,
SpecimenImportConfiguratorBase config) |
void |
SpecimenImportReport.addIndividualAssociation(Taxon taxon,
java.lang.String derivedUnitId,
DerivedUnit derivedUnitBase) |
static java.lang.String |
AbcdImportUtility.getUnitID(DerivedUnit derivedUnit,
Abcd206ImportConfigurator config) |
static java.lang.String |
SpecimenImportUtility.getUnitID(DerivedUnit derivedUnit,
SpecimenImportConfiguratorBase config) |
static void |
AbcdImportUtility.setUnitID(DerivedUnit derivedUnit,
java.lang.String unitId,
Abcd206ImportConfigurator config) |
static void |
SpecimenImportUtility.setUnitID(DerivedUnit derivedUnit,
java.lang.String unitId,
Abcd206ImportConfigurator config) |
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
GbifImportState.getDerivedUnitBase() |
Modifier and Type | Method and Description |
---|---|
void |
GbifImportState.setDerivedUnitBase(DerivedUnit derivedUnitBase) |
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
SimpleSpecimen.getSpecimen() |
Modifier and Type | Method and Description |
---|---|
void |
SimpleSpecimen.setSpecimen(DerivedUnit specimen) |
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
TaxonXExtractor.MySpecimenOrObservation.getDerivedUnitBase() |
Modifier and Type | Method and Description |
---|---|
protected void |
TaxonXAddSources.addAndSaveSource(Reference refMods,
DerivedUnit derivedUnitBase) |
protected TaxonXExtractor.MySpecimenOrObservation |
TaxonXExtractor.extractSpecimenOrObservation(org.w3c.dom.Node specimenObservationNode,
DerivedUnit derivedUnitBase,
SpecimenOrObservationType defaultAssociation,
TaxonName typifiableName) |
void |
TaxonXExtractor.MySpecimenOrObservation.setDerivedUnitBase(DerivedUnit derivedUnitBase) |
Modifier and Type | Class and Description |
---|---|
class |
DnaSample
A DNA Sample is the extracted DNA of a given tissue sample.
|
Modifier and Type | Method and Description |
---|---|
DerivedUnit |
SpecimenTypeDesignation.getTypeSpecimen()
Returns the
derived unit (specimen or figure) that is used
in this specimen type designation to typify the taxon name . |
Modifier and Type | Method and Description |
---|---|
SpecimenTypeDesignation |
TaxonName.addSpecimenTypeDesignation(DerivedUnit typeSpecimen,
SpecimenTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean isNotDesignated,
boolean addToAllHomotypicNames)
Creates and adds a new
specimen type designation
to this taxon name's set of type designations. |
SpecimenTypeDesignation |
ITaxonNameBase.addSpecimenTypeDesignation(DerivedUnit typeSpecimen,
SpecimenTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean isNotDesignated,
boolean addToAllHomotypicNames)
Creates and adds a new
specimen type designation
to this taxon name's set of type designations. |
void |
SpecimenTypeDesignation.setTypeSpecimen(DerivedUnit typeSpecimen) |
Constructor and Description |
---|
SpecimenTypeDesignation(DerivedUnit specimen,
SpecimenTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean isNotDesignated)
Class constructor: creates a new specimen type designation instance
(including its
reference source and
eventually the taxon name string originally used by this reference when
establishing the former designation). |
Modifier and Type | Class and Description |
---|---|
class |
MediaSpecimen
Instances of MediaSpecimen represent a specimen which IS a media (photo, drawing, ...).
|
Modifier and Type | Field and Description |
---|---|
protected java.util.Set<DerivedUnit> |
DerivationEvent.derivatives |
Modifier and Type | Method and Description |
---|---|
static DerivedUnit |
DerivedUnit.NewInstance(SpecimenOrObservationType type) |
static DerivedUnit |
DerivedUnit.NewPreservedSpecimenInstance()
Factory method
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<DerivedUnit> |
DerivationEvent.getDerivatives()
The specimen or observations that are the output for this derviation event.
|
Modifier and Type | Method and Description |
---|---|
void |
DerivationEvent.addDerivative(DerivedUnit derivative)
Adds a new output specimen or observation for this derivation event.
|
static DerivationEvent |
DerivationEvent.NewSimpleInstance(SpecimenOrObservationBase original,
DerivedUnit derivative,
DerivationEventType type)
Factory method
|
void |
DerivationEvent.removeDerivative(DerivedUnit derivative)
Removes an output specimen or observation for this derviation event.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<UuidAndTitleCache<DerivedUnit>> |
OccurrenceDaoHibernateImpl.getDerivedUnitUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
Modifier and Type | Method and Description |
---|---|
java.util.List<UuidAndTitleCache<DerivedUnit>> |
IOccurrenceDao.getDerivedUnitUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern)
Retrieves the
UUID and the string representation (title cache) of all
DerivedUnit s found in the data base. |
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